diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 4203543..7dfbb24 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -45,8 +45,8 @@ jobs: - name: Fetch Output run: | - scp raina.ans@login-00.discovery.neu.edu:/home/raina.ans/R/job_output.txt job_output.txt - scp raina.ans@login-00.discovery.neu.edu:/home/raina.ans/R/job_error.txt job_error.txt + scp raina.ans@login-00.discovery.neu.edu:/work/VitekLab/Projects/Benchmarking/job_output.txt job_output.txt + scp raina.ans@login-00.discovery.neu.edu:/work/VitekLab/Projects/Benchmarking/job_error.txt job_error.txt - name: Upload Output as Artifact uses: actions/upload-artifact@v4 diff --git a/benchmark/benchmark.R b/benchmark/benchmark.R index 650c700..40cb311 100644 --- a/benchmark/benchmark.R +++ b/benchmark/benchmark.R @@ -123,11 +123,11 @@ data_process_tasks <- list( ), list( label = "Data process without Normalization", - result = function() dataProcess(msstats_format, normalization = "FALSE", n_top_feature = 20) + result = function() dataProcess(msstats_format, featureSubset = "topN", normalization = "FALSE", n_top_feature = 20) ), list( label = "Data process without Normalization with MBImpute False", - result = function() dataProcess(msstats_format, normalization = "FALSE", n_top_feature = 20, MBimpute = FALSE) + result = function() dataProcess(msstats_format, featureSubset = "topN", normalization = "FALSE", n_top_feature = 20, MBimpute = FALSE) ) ) diff --git a/benchmark/config.slurm b/benchmark/config.slurm index 8a5d955..520857b 100644 --- a/benchmark/config.slurm +++ b/benchmark/config.slurm @@ -1,7 +1,7 @@ #!/bin/bash #SBATCH --job-name=msstats_benchmark_job -#SBATCH --output=job_output.txt -#SBATCH --error=job_error.txt +#SBATCH --output=/work/VitekLab/Projects/Benchmarking/job_output.txt +#SBATCH --error=/work/VitekLab/Projects/Benchmarking/job_error.txt #SBATCH --time=01:00:00 # Set the maximum run time #SBATCH --ntasks=1 # Number of tasks (one process) #SBATCH --cpus-per-task=8 # Use 8 CPU cores for the task